Cytoscape Wiki|
← Revision 3 as of 2009-04-20 01:24:23
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← Revision 4 as of 2009-04-20 18:51:00 →
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''Description:'' The core network and data table models used by everyone else. ''Status:'' The API and an implementation are largely complete. ''Who has done the work:'' UCSD with lots of feedback from others |
||''Description:'' ||The core network and data table models used by everyone else.|| ||''3.0 Status:'' ||The API and an implementation are largely complete.|| ||''Who has done the work in 3.0:'' ||UCSD with lots of feedback from others|| ||''Who did the work in 2.x:'' ||everyone|| |
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''Description:'' An API for definining and executing Tasks, configuring the Tasks, and supporting undo. ''Status:'' The API and an implementation are largely complete. ''Who has done the work:'' Pasteur, UCSD |
||''Description:'' ||An API for definining and executing Tasks, configuring the Tasks, and supporting undo.|| ||''3.0 Status:'' ||The API and an implementation are largely complete.|| ||''Who has done the work in 3.0:'' ||Pasteur, UCSD|| ||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)|| |
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''Description:'' Both developer and user logging framework. ''Status:'' Incomplete. ''Who has done the work:'' ??? |
||''Description:'' ||Both developer and user logging framework.|| ||''3.0 Status:'' ||Incomplete.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||UCSF, ISB|| |
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''Description:'' APIs for importing and exporting data including networks, tables, sessions, and images. ''Status:'' The API is largely defined, but all implementations need to be refined. ''Who has done the work:'' UCSD, Pasteur, Toronto |
||''Description:'' ||APIs for importing and exporting data including networks, tables, sessions, and images.|| ||''3.0 Status:'' ||The API is largely defined, but all implementations need to be refined.|| ||''Who has done the work in 3.0:'' ||UCSD, Pasteur, Toronto|| ||''Who did the work in 2.x:'' ||everyone|| |
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''Description:'' An API that '''''defines''''' the visualization of a network (and later table), but doesn't actually do the rendering. ''Status:'' The API and implementation are largely complete. ''Who has done the work:'' UCSD, Daniel Abel |
||''Description:'' ||An API that '''''defines''''' the visualization of a network (and later table), but doesn't actually do the rendering.|| ||''3.0 Status:'' ||The API and implementation are largely complete.|| ||''Who has done the work in 3.0:'' ||UCSD, Daniel Abel|| ||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)|| |
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''Description:'' An API that modifies a view-model based on attribute (data table) values. ''Status:'' The API is largely complete and the user interface implementation is nearing completion. ''Who has done the work:'' UCSD |
||''Description:'' ||An API that modifies a view-model based on attribute (data table) values.|| ||''3.0 Status:'' ||The API is largely complete and the user interface implementation is nearing completion.|| ||''Who has done the work in 3.0:'' ||UCSD|| ||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)|| |
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''Description:'' An implementation that renders (to screen, to image file, to ??) a network whose visualization is defined by a view-model. ''Status:'' The API has been sketched and an implementation is in place, but it needs a lot of refinement. ''Who has done the work:'' UCSD |
||''Description:'' ||An implementation that renders (to screen, to image file, to ??) a network whose visualization is defined by a view-model.|| ||''3.0 Status:'' ||The API has been sketched and an implementation is in place, but it needs a lot of refinement.|| ||''Who has done the work in 3.0:'' ||UCSD|| ||''Who did the work in 2.x:'' ||everyone|| |
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''Description:'' An implementation that renders a data table. ''Status:'' Incomplete. ''Who has done the work:'' ??? |
||''Description:'' ||An implementation that renders a data table.|| ||''3.0 Status:'' ||Incomplete. || ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||UCSD, others|| |
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''Description:'' A user interface that allows users to add, delete, and change nodes and edges in a network. ''Status:'' Incomplete. ''Who has done the work:'' Agilent |
||''Description:'' ||A user interface that allows users to add, delete, and change nodes and edges in a network.|| ||''3.0 Status:'' ||Incomplete.|| ||''Who has done the work in 3.0:'' ||??? || ||''Who did the work in 2.x:'' ||Agilent|| |
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''Description:'' An API and several implementations of layout algorithms that modify the view-model for a given network. ''Status:'' Incomplete. ''Who has done the work:'' UCSF, UCSD |
||''Description:'' ||An API and several implementations of layout algorithms that modify the view-model for a given network.|| ||''3.0 Status:'' ||Incomplete.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||UCSF, UCSD|| |
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''Description:'' An API and user interface that allows a network to be searched and/or filtered. ''Status:'' Incomplete. ''Who has done the work:'' UCSD |
||''Description:'' ||An API and user interface that allows a network to be searched and/or filtered.|| ||''3.0 Status:'' ||Incomplete.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||MSKCC, Maital Ashkenazi, UCSD|| |
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''Description:'' An API and user interface that allows groups of nodes to be defined and captured as subnetworks. ''Status:'' Incomplete. ''Who has done the work:'' UCSF |
||''Description:'' ||An API and user interface that allows groups of nodes to be defined and captured as subnetworks.|| ||''3.0 Status:'' ||Incomplete.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||UCSF|| |
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''Description:'' An API that provides for set operations on networks based on attributes of the networks. ''Status:'' Incomplete. ''Who has done the work:'' UCSD |
||''Description:'' ||An API that provides for set operations on networks based on attributes of the networks.|| ||''3.0 Status:'' ||Incomplete.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||UCSD|| |
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''Description:'' An API that allows objects in Cytoscape to be linked to web databases. ''Status:'' Incomplete. ''Who has done the work:'' MSKCC, Agilent (support via right-mouse menu handler) |
||''Description:'' ||An API that allows objects in Cytoscape to be linked to web databases.|| ||''3.0 Status:'' ||Incomplete.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||MSKCC, Agilent|| |
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''Description:'' An API that provides a common interface for accessing web based interaction databases. ''Status:'' Some work has been done, but incomplete. ''Who has done the work:'' UCSD |
||''Description:'' ||An API that provides a common interface for accessing web based interaction databases.|| ||''3.0 Status:'' ||Some work has been done, but incomplete.|| ||''Who has done the work in 3.0:'' ||UCSD|| ||''Who did the work in 2.x:'' ||MSKCC, Toronto, UCSD|| |
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''Description:'' An API that allows scripts written in other programming languages (Python, Groovy, Javascript, etc.) to access and use the Cytoscape API. ''Status:'' Incomplete. ''Who has done the work:'' UCSD |
||''Description:'' ||An API that allows scripts written in other programming languages (Python, Groovy, Javascript, etc.) to access and use the Cytoscape API.|| ||''3.0 Status:'' ||Incomplete.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||UCSF, UCSD|| |
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''Description:'' A Java Swing-based desktop application for visualizing and analyzing networks (what everyone knows today as "Cytoscape"). ''Status:'' About 75% complete (excluding core plugins). ''Who has done the work:'' UCSD |
||''Description:'' ||A Java Swing-based desktop application for visualizing and analyzing networks (what everyone knows today as "Cytoscape").|| ||''3.0 Status:'' ||About 75% complete (excluding core plugins).|| ||''Who has done the work in 3.0:'' ||UCSD|| ||''Who did the work in 2.x:'' ||everyone|| |
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''Description:'' A command-line application built from low-level cytoscape modules that can perform various tasks (e.g. load a networks, lay it out, and render it to an image file) without the need for a graphical user interface. ''Status:'' Incomplete. ''Who has done the work:'' ??? |
||''Description:'' ||A command-line application built from low-level cytoscape modules that can perform various tasks (e.g. load a networks, lay it out, and render it to an image file) without the need for a graphical user interface.|| ||''3.0 Status:'' ||Incomplete.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)|| |
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''Description:'' A user interface for downloading, installing, automatic-update, and otherwise managing cytoscape bundles. ''Status:'' The user interface is largely finished, but still needs to be integrated with the swing application. ''Who has done the work:'' UCSD |
||''Description:'' ||A user interface for downloading, installing, automatic-update, and otherwise managing cytoscape bundles.|| ||''3.0 Status:'' ||The user interface is largely finished, but still needs to be integrated with the swing application.|| ||''Who has done the work in 3.0:'' ||UCSD|| ||''Who did the work in 2.x:'' ||ISB, UCSD|| |
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''Description:'' The management and oversight of the development, planning, and execution of unit tests, functional tests, acceptance tests, performance tests, and general promotion of "quality." ''Status:'' Incomplete. ''Who has done the work:'' ??? |
||''Description:'' ||The management and oversight of the development, planning, and execution of unit tests, functional tests, acceptance tests, performance tests, and general promotion of "quality."|| ||''3.0 Status:'' ||Incomplete.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||There are a few unit tests scattered about contributed by different groups, but no comprehensive strategy.|| |
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''Description:'' The management and oversight of the overall Cytoscape architecture and how different modules interact with one another. ''Status:'' It exists, but is poorly documented. ''Who has done the work:'' UCSD |
||''Description:'' ||The management and oversight of the overall Cytoscape architecture and how different modules interact with one another.|| ||''3.0 Status:'' ||It exists, but is poorly documented.|| ||''Who has done the work in 3.0:'' ||UCSD|| ||''Who did the work in 2.x:'' ||everyone|| |
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''Description:'' The management and oversight of documentation for Cytoscape including the website, user manuals, tutorials, developer documents, wikis, and API documention. ''Status:'' Incomplete. ''Who has done the work:'' ??? |
||''Description:'' ||The management and oversight of documentation for Cytoscape including the website, user manuals, tutorials, developer documents, wikis, and API documention.|| ||''3.0 Status:'' ||Incomplete.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||everyone|| |
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''Description:'' The management and oversight of the development processes, build tools, release tools and processes for Cytoscape. ''Status:'' Ongoing. ''Who has done the work:'' UCSD, ??? |
||''Description:'' ||The management and oversight of the development processes, build tools, release tools and processes for Cytoscape.|| ||''3.0 Status:'' ||Ongoing.|| ||''Who has done the work in 3.0:'' ||ISB, Toronto, UCSD|| ||''Who did the work in 2.x:'' ||everyone|| |
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| ''Description:'' The evaluation and refinement of Cytoscape usability including usability testing and tracking. |
||''Description:'' ||The evaluation and refinement of Cytoscape usability including usability testing and tracking.|| ||''3.0 Status:'' ||Inactive.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||Pasteur, ???|| |
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''Status:'' Inactive. ''Who has done the work:'' ??? |
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''Description:'' A future project for providing enhanced visualizations of networks in cytoscape with other background and foreground graphics and text (e.g. cell location). ''Status:'' Future project. ''Who has done the work:'' UCSF, MSKCC/Agilent (via changes to canvas object) |
||''Description:'' ||A future project for providing enhanced visualizations of networks in cytoscape with other background and foreground graphics and text (e.g. cell location).|| ||''3.0 Status:'' ||Future project.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||UCSF, MSKCC, Agilent|| |
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''Description:'' A future project for a web front end for Cytoscape. ''Status:'' None for the Cytoscape Consortium, but various member organizations are developing independent projects. ''Who has done the work:'' ISB, Toronto |
||''Description:'' ||A future project for a web front end for Cytoscape.|| ||''3.0 Status:'' ||None for the Cytoscape Consortium, but various member organizations are developing independent projects.|| ||''Who has done the work in 3.0:'' ||ISB, Toronto|| ||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)|| |
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''Description:'' A future project that will provide a relational (or other) database backend for Cytoscape. ''Status:'' Future project. ''Who has done the work:'' ??? |
||''Description:'' ||A future project that will provide a relational (or other) database backend for Cytoscape.|| ||''3.0 Status:'' ||Future project.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)|| |
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''Description:'' A future project that extends the interface for CyDataTable to allow things like joins and other relational database capabilities. ''Status:'' Future project. ''Who has done the work:'' ??? |
||''Description:'' ||A future project that extends the interface for CyDataTable to allow things like joins and other relational database capabilities.|| ||''3.0 Status:'' ||Future project.|| ||''Who has done the work in 3.0:'' ||???|| ||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)|| |
Cytoscape 3.0 (and beyond) Development Modules
model
Description: |
The core network and data table models used by everyone else. |
3.0 Status: |
The API and an implementation are largely complete. |
Who has done the work in 3.0: |
UCSD with lots of feedback from others |
Who did the work in 2.x: |
everyone |
work
Description: |
An API for definining and executing Tasks, configuring the Tasks, and supporting undo. |
3.0 Status: |
The API and an implementation are largely complete. |
Who has done the work in 3.0: |
Pasteur, UCSD |
Who did the work in 2.x: |
(didn't exist prior to 3.0) |
logging
Description: |
Both developer and user logging framework. |
3.0 Status: |
Incomplete. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
UCSF, ISB |
io
Description: |
APIs for importing and exporting data including networks, tables, sessions, and images. |
3.0 Status: |
The API is largely defined, but all implementations need to be refined. |
Who has done the work in 3.0: |
UCSD, Pasteur, Toronto |
Who did the work in 2.x: |
everyone |
view-model
Description: |
An API that defines the visualization of a network (and later table), but doesn't actually do the rendering. |
3.0 Status: |
The API and implementation are largely complete. |
Who has done the work in 3.0: |
UCSD, Daniel Abel |
Who did the work in 2.x: |
(didn't exist prior to 3.0) |
vizmap
Description: |
An API that modifies a view-model based on attribute (data table) values. |
3.0 Status: |
The API is largely complete and the user interface implementation is nearing completion. |
Who has done the work in 3.0: |
UCSD |
Who did the work in 2.x: |
(didn't exist prior to 3.0) |
presentation
Description: |
An implementation that renders (to screen, to image file, to ??) a network whose visualization is defined by a view-model. |
3.0 Status: |
The API has been sketched and an implementation is in place, but it needs a lot of refinement. |
Who has done the work in 3.0: |
UCSD |
Who did the work in 2.x: |
everyone |
attribute-presentation
Description: |
An implementation that renders a data table. |
3.0 Status: |
Incomplete. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
UCSD, others |
editor
Description: |
A user interface that allows users to add, delete, and change nodes and edges in a network. |
3.0 Status: |
Incomplete. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
Agilent |
layout
Description: |
An API and several implementations of layout algorithms that modify the view-model for a given network. |
3.0 Status: |
Incomplete. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
UCSF, UCSD |
search/filters
Description: |
An API and user interface that allows a network to be searched and/or filtered. |
3.0 Status: |
Incomplete. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
MSKCC, Maital Ashkenazi, UCSD |
groups
Description: |
An API and user interface that allows groups of nodes to be defined and captured as subnetworks. |
3.0 Status: |
Incomplete. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
UCSF |
merge
Description: |
An API that provides for set operations on networks based on attributes of the networks. |
3.0 Status: |
Incomplete. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
UCSD |
linkout
Description: |
An API that allows objects in Cytoscape to be linked to web databases. |
3.0 Status: |
Incomplete. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
MSKCC, Agilent |
webservices
Description: |
An API that provides a common interface for accessing web based interaction databases. |
3.0 Status: |
Some work has been done, but incomplete. |
Who has done the work in 3.0: |
UCSD |
Who did the work in 2.x: |
MSKCC, Toronto, UCSD |
scripting
Description: |
An API that allows scripts written in other programming languages (Python, Groovy, Javascript, etc.) to access and use the Cytoscape API. |
3.0 Status: |
Incomplete. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
UCSF, UCSD |
swing-application
Description: |
A Java Swing-based desktop application for visualizing and analyzing networks (what everyone knows today as "Cytoscape"). |
3.0 Status: |
About 75% complete (excluding core plugins). |
Who has done the work in 3.0: |
UCSD |
Who did the work in 2.x: |
everyone |
command-line-application
Description: |
A command-line application built from low-level cytoscape modules that can perform various tasks (e.g. load a networks, lay it out, and render it to an image file) without the need for a graphical user interface. |
3.0 Status: |
Incomplete. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
(didn't exist prior to 3.0) |
plugin-manager
Description: |
A user interface for downloading, installing, automatic-update, and otherwise managing cytoscape bundles. |
3.0 Status: |
The user interface is largely finished, but still needs to be integrated with the swing application. |
Who has done the work in 3.0: |
UCSD |
Who did the work in 2.x: |
ISB, UCSD |
qa/testing
Description: |
The management and oversight of the development, planning, and execution of unit tests, functional tests, acceptance tests, performance tests, and general promotion of "quality." |
3.0 Status: |
Incomplete. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
There are a few unit tests scattered about contributed by different groups, but no comprehensive strategy. |
architecture
Description: |
The management and oversight of the overall Cytoscape architecture and how different modules interact with one another. |
3.0 Status: |
It exists, but is poorly documented. |
Who has done the work in 3.0: |
UCSD |
Who did the work in 2.x: |
everyone |
documentation
Description: |
The management and oversight of documentation for Cytoscape including the website, user manuals, tutorials, developer documents, wikis, and API documention. |
3.0 Status: |
Incomplete. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
everyone |
dev-process
Description: |
The management and oversight of the development processes, build tools, release tools and processes for Cytoscape. |
3.0 Status: |
Ongoing. |
Who has done the work in 3.0: |
ISB, Toronto, UCSD |
Who did the work in 2.x: |
everyone |
usability
Description: |
The evaluation and refinement of Cytoscape usability including usability testing and tracking. |
3.0 Status: |
Inactive. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
Pasteur, ??? |
decorated-networks
Description: |
A future project for providing enhanced visualizations of networks in cytoscape with other background and foreground graphics and text (e.g. cell location). |
3.0 Status: |
Future project. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
UCSF, MSKCC, Agilent |
web-application
Description: |
A future project for a web front end for Cytoscape. |
3.0 Status: |
None for the Cytoscape Consortium, but various member organizations are developing independent projects. |
Who has done the work in 3.0: |
ISB, Toronto |
Who did the work in 2.x: |
(didn't exist prior to 3.0) |
database-backend
Description: |
A future project that will provide a relational (or other) database backend for Cytoscape. |
3.0 Status: |
Future project. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
(didn't exist prior to 3.0) |
extended-cydatatable
Description: |
A future project that extends the interface for CyDataTable to allow things like joins and other relational database capabilities. |
3.0 Status: |
Future project. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
(didn't exist prior to 3.0) |